Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001046.1 Hibiscus syriacus cultivar Beakdansim tig00002075_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 125993
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3905 original size:15 final size:15
Alignment explanation
Indices: 3885--3916 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3875 TTAAGACCTT
3885 TCGATTTTAAAAATA
1 TCGATTTTAAAAATA
3900 TCGATTTTAAAAATA
1 TCGATTTTAAAAATA
3915 TC
1 TC
3917 TTTGATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (15 bp):
TCGATTTTAAAAATA
Found at i:6623 original size:2 final size:2
Alignment explanation
Indices: 6616--6743 Score: 62
Period size: 2 Copynumber: 60.0 Consensus size: 2
6606 TGTCTATATT
* * * * *
6616 TC TC TC TC TC AT- TC TC TC CC AC TA TC TC TC TC ATG T- TC TC TT
1 TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC
* *
6658 TA TC TC TC GTAC TC TC TC TC TC TC GTAC TC TC TC TC TC CC TC TC
1 TC TC TC TC -T-C TC TC TC TC TC TC -T-C TC TC TC TC TC TC TC TC
* * *
6702 TC GTAC TC TA TC TC TC TC CC TC TC TC GTAC TC TA TC TC TC TC
1 TC -T-C TC TC TC TC TC TC TC TC TC TC -T-C TC TC TC TC TC TC
6744 ACCCACTCTT
Statistics
Matches: 97, Mismatches: 17, Indels: 24
0.70 0.12 0.17
Matches are distributed among these distances:
1 2 0.02
2 81 0.84
3 10 0.10
4 4 0.04
ACGTcount: A:0.09, C:0.43, G:0.04, T:0.45
Consensus pattern (2 bp):
TC
Found at i:6694 original size:22 final size:22
Alignment explanation
Indices: 6669--6741 Score: 110
Period size: 22 Copynumber: 3.2 Consensus size: 22
6659 ATCTCTCGTA
*
6669 CTCTCTCTCTCTCGTACTCTCT
1 CTCTCCCTCTCTCGTACTCTCT
6691 CTCTCCCTCTCTCGTACTCTATCT
1 CTCTCCCTCTCTCGTACTC--TCT
*
6715 CTCTCCCTCTCTCGTACTCTAT
1 CTCTCCCTCTCTCGTACTCTCT
6737 CTCTC
1 CTCTC
6742 TCACCCACTC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
22 25 0.53
24 22 0.47
ACGTcount: A:0.07, C:0.47, G:0.04, T:0.42
Consensus pattern (22 bp):
CTCTCCCTCTCTCGTACTCTCT
Found at i:6710 original size:16 final size:16
Alignment explanation
Indices: 6660--6743 Score: 86
Period size: 16 Copynumber: 5.4 Consensus size: 16
6650 GTTCTCTTTA
6660 TCTCTCGTACTCTCTC
1 TCTCTCGTACTCTCTC
6676 TCTCTCGTACTCTCTC
1 TCTCTCGTACTCTCTC
*
6692 TCTC-CCT-CTCTCGTAC
1 TCTCTCGTACTCTC-T-C
* *
6708 TCTATC-T-CTCTCCC
1 TCTCTCGTACTCTCTC
*
6722 TCTCTCGTACTCTATC
1 TCTCTCGTACTCTCTC
6738 TCTCTC
1 TCTCTC
6744 ACCCACTCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
14 11 0.19
15 4 0.07
16 41 0.72
17 1 0.02
ACGTcount: A:0.07, C:0.45, G:0.05, T:0.43
Consensus pattern (16 bp):
TCTCTCGTACTCTCTC
Found at i:6742 original size:24 final size:24
Alignment explanation
Indices: 6669--6743 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
6659 ATCTCTCGTA
*
6669 CTCTCTCTCTCTCGTACTC--TCT
1 CTCTCCCTCTCTCGTACTCTATCT
6691 CTCTCCCTCTCTCGTACTCTATCT
1 CTCTCCCTCTCTCGTACTCTATCT
6715 CTCTCCCTCTCTCGTACTCTATCT
1 CTCTCCCTCTCTCGTACTCTATCT
6739 CTCTC
1 CTCTC
6744 ACCCACTCTT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
22 18 0.36
24 32 0.64
ACGTcount: A:0.07, C:0.47, G:0.04, T:0.43
Consensus pattern (24 bp):
CTCTCCCTCTCTCGTACTCTATCT
Found at i:6960 original size:22 final size:22
Alignment explanation
Indices: 6935--6982 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
6925 CTTGCCCATT
*
6935 CTCTCTCTTTCTCTCTCCCCTA
1 CTCTATCTTTCTCTCTCCCCTA
6957 CTCTATCTTTCTCTCTCCCCTA
1 CTCTATCTTTCTCTCTCCCCTA
6979 CTCT
1 CTCT
6983 TCGTCTCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.06, C:0.48, G:0.00, T:0.46
Consensus pattern (22 bp):
CTCTATCTTTCTCTCTCCCCTA
Found at i:6989 original size:20 final size:22
Alignment explanation
Indices: 6935--6992 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
6925 CTTGCCCATT
* *
6935 CTCTCTCTTTCTCTCTCCCCTA
1 CTCTATCTGTCTCTCTCCCCTA
*
6957 CTCTATCTTTCTCTCTCCCCTA
1 CTCTATCTGTCTCTCTCCCCTA
6979 CTCT-TC-GTCTCTCT
1 CTCTATCTGTCTCTCT
6993 TACCCACTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.21
21 2 0.06
22 25 0.74
ACGTcount: A:0.05, C:0.47, G:0.02, T:0.47
Consensus pattern (22 bp):
CTCTATCTGTCTCTCTCCCCTA
Found at i:7294 original size:8 final size:8
Alignment explanation
Indices: 7281--7305 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
7271 TCTTTTTTCC
7281 CTCACTCT
1 CTCACTCT
7289 CTCACTCT
1 CTCACTCT
7297 CTCACTCT
1 CTCACTCT
7305 C
1 C
7306 GCCCACTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.52, G:0.00, T:0.36
Consensus pattern (8 bp):
CTCACTCT
Found at i:8680 original size:20 final size:24
Alignment explanation
Indices: 8632--8680 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 24
8622 ACATACTTTC
*
8632 TATTTACTTTTTCTTCCTTTTGTT
1 TATTTACTTTTTCTTCCTTTTGAT
8656 TATTT-CTTTTT-TT-CTTTT-AT
1 TATTTACTTTTTCTTCCTTTTGAT
8676 TATTT
1 TATTT
8681 TTTCCTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 5 0.21
22 2 0.08
23 6 0.25
24 5 0.21
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (24 bp):
TATTTACTTTTTCTTCCTTTTGAT
Found at i:8749 original size:2 final size:2
Alignment explanation
Indices: 8742--8784 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
8732 CATAACGTTT
8742 TA TA TA TA TA T- TA T- TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
8782 TA T
1 TA T
8785 TAGTTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 3 0.08
2 33 0.89
3 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:8854 original size:14 final size:13
Alignment explanation
Indices: 8838--9053 Score: 63
Period size: 12 Copynumber: 17.6 Consensus size: 13
8828 TTTAACCTAA
8838 TATATTTATTTAT
1 TATATTTATTTAT
*
8851 ATATATATTTTTTAT
1 -TATAT-TTATTTAT
8866 TAT-TTTA-TTATT
1 TATATTTATTTA-T
* *
8878 TCTATTTTTTTAT
1 TATATTTATTTAT
8891 TATA-TTA-TTAT
1 TATATTTATTTAT
* *
8902 TATGTTTTTATTAT
1 TATATTTAT-TTAT
*
8916 TATTTTTCATTT-T
1 TATATTT-ATTTAT
*
8929 TTTATTT-TTT-T
1 TATATTTATTTAT
*
8940 TAT-TTTTTTTAT
1 TATATTTATTTAT
* *
8952 T-T-TTTTTTTTT
1 TATATTTATTTAT
* *
8963 TTTATTTTTTTAT
1 TATATTTATTTAT
*
8976 T-TTTTTATTT-T
1 TATATTTATTTAT
*
8987 TTTATTT-TTTAT
1 TATATTTATTTAT
* *
8999 T-T-TTTTTTTTT
1 TATATTTATTTAT
* *
9010 TTTATTTTTTTAT
1 TATATTTATTTAT
*
9023 T-TTTTTATTT-T
1 TATATTTATTTAT
* * *
9034 TTTATTTTTTTCT
1 TATATTTATTTAT
9047 TA-ATTTA
1 TATATTTA
9054 ATTAACTTAT
Statistics
Matches: 157, Mismatches: 26, Indels: 40
0.70 0.12 0.18
Matches are distributed among these distances:
10 6 0.04
11 42 0.27
12 44 0.28
13 34 0.22
14 23 0.15
15 8 0.05
ACGTcount: A:0.18, C:0.01, G:0.00, T:0.81
Consensus pattern (13 bp):
TATATTTATTTAT
Found at i:8868 original size:22 final size:21
Alignment explanation
Indices: 8843--8952 Score: 70
Period size: 21 Copynumber: 5.1 Consensus size: 21
8833 CCTAATATAT
8843 TTATTTATATATATATTTTTTA
1 TTATTTATATAT-TATTTTTTA
*
8865 TTATTTTATTATTTCTATTTTTTTA
1 TTA-TTTA-TATAT-TA-TTTTTTA
8890 TTATATTAT-TATTATGTTTTTA
1 TTAT-TTATATATTAT-TTTTTA
*
8912 TTA-TTAT-TTTTCATTTTTTTA
1 TTATTTATATATT-A-TTTTTTA
*
8933 TT-TTT-TTTATT-TTTTTTA
1 TTATTTATATATTATTTTTTA
8951 TT
1 TT
8953 TTTTTTTTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 22
0.73 0.05 0.22
Matches are distributed among these distances:
18 9 0.12
20 8 0.11
21 15 0.20
22 15 0.20
23 6 0.08
24 8 0.11
25 13 0.18
ACGTcount: A:0.22, C:0.02, G:0.01, T:0.75
Consensus pattern (21 bp):
TTATTTATATATTATTTTTTA
Found at i:8873 original size:8 final size:8
Alignment explanation
Indices: 8858--9044 Score: 232
Period size: 8 Copynumber: 22.8 Consensus size: 8
8848 TATATATATA
8858 TTTTTTAT
1 TTTTTTAT
*
8866 TATTTTAT
1 TTTTTTAT
*
8874 TATTTCTAT
1 T-TTTTTAT
8883 TTTTTTAT
1 TTTTTTAT
* *
8891 TATATTAT
1 TTTTTTAT
* * *
8899 TATTATGT
1 TTTTTTAT
8907 TTTTATTAT
1 TTTT-TTAT
8916 TATTTTTCAT
1 T-TTTTT-AT
8926 TTTTTTATT
1 TTTTTTA-T
8935 TTTTTTATT
1 TTTTTTA-T
8944 TTTTTTAT
1 TTTTTTAT
*
8952 TTTTTTTT
1 TTTTTTAT
8960 TTTTTTAT
1 TTTTTTAT
8968 TTTTTTAT
1 TTTTTTAT
8976 TTTTTTAT
1 TTTTTTAT
8984 TTTTTTA-
1 TTTTTTAT
8991 TTTTTTAT
1 TTTTTTAT
*
8999 TTTTTTTT
1 TTTTTTAT
9007 TTTTTTAT
1 TTTTTTAT
9015 TTTTTTAT
1 TTTTTTAT
9023 TTTTTTAT
1 TTTTTTAT
9031 TTTTTTAT
1 TTTTTTAT
9039 TTTTTT
1 TTTTTT
9045 CTTAATTTAA
Statistics
Matches: 157, Mismatches: 16, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
7 7 0.04
8 111 0.71
9 33 0.21
10 6 0.04
ACGTcount: A:0.14, C:0.01, G:0.01, T:0.84
Consensus pattern (8 bp):
TTTTTTAT
Found at i:8929 original size:1 final size:1
Alignment explanation
Indices: 8925--9044 Score: 132
Period size: 1 Copynumber: 120.0 Consensus size: 1
8915 TTATTTTTCA
* * * * * *
8925 TTTTTTTATTTTTTTTATTTTTTTTATTTTTTTTTTTTTTTATTTTTTTATTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * *
8990 ATTTTTTATTTTTTTTTTTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9045 CTTAATTTAA
Statistics
Matches: 95, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 95 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:23403 original size:9 final size:10
Alignment explanation
Indices: 23377--23402 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
23367 TTGTTTAAAT
23377 TTTTTTTAGA
1 TTTTTTTAGA
23387 TTTTTTTAGA
1 TTTTTTTAGA
23397 TTTTTT
1 TTTTTT
23403 AACATTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (10 bp):
TTTTTTTAGA
Found at i:25937 original size:2 final size:2
Alignment explanation
Indices: 25926--25997 Score: 128
Period size: 2 Copynumber: 36.0 Consensus size: 2
25916 TAATCATTTA
25926 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25967 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
25998 TTCTGATATT
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.01
2 65 0.96
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31825 original size:63 final size:63
Alignment explanation
Indices: 31722--31853 Score: 246
Period size: 63 Copynumber: 2.1 Consensus size: 63
31712 ACATGACATC
* *
31722 GGTTTCTCATATATTACTGAACTAACATTGTTTTTCAATTTAATTTCAAGTGTGCTAGAAGAT
1 GGTTTGTCATATATTACTGAACTAACATTGTTTTTAAATTTAATTTCAAGTGTGCTAGAAGAT
31785 GGTTTGTCATATATTACTGAACTAACATTGTTTTTAAATTTAATTTCAAGTGTGCTAGAAGAT
1 GGTTTGTCATATATTACTGAACTAACATTGTTTTTAAATTTAATTTCAAGTGTGCTAGAAGAT
31848 GGTTTG
1 GGTTTG
31854 ATGAATATGA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (63 bp):
GGTTTGTCATATATTACTGAACTAACATTGTTTTTAAATTTAATTTCAAGTGTGCTAGAAGAT
Found at i:39816 original size:59 final size:59
Alignment explanation
Indices: 39673--39869 Score: 220
Period size: 59 Copynumber: 3.3 Consensus size: 59
39663 TTTTAACAAA
**
39673 GGGTGACC-AAATAGAACCAAAATGTAACATTGAGTGCGATTTTG-AAAAAAAATAATT
1 GGGTGACCAAAATAGAACCAAAATGTAACATTGAGTATGATTTTGAAAAAAAAATAATT
* * * * * *
39730 GGGTAACCAAAATAGAATCAAATTGTAACATTGTGTTTGATTTTGAAAAAAAAATATTT
1 GGGTGACCAAAATAGAACCAAAATGTAACATTGAGTATGATTTTGAAAAAAAAATAATT
* * * * *
39789 GGGTGACCAAAACAGAAGCAAAATGTAAC-TTTACATATGATTTTGAGAAAAAAATATAGTT
1 GGGTGACCAAAATAGAACCAAAATGTAACATTGA-GTATGATTTTGA-AAAAAAA-ATAATT
*
39850 GGATGACCAAAATAGAACCA
1 GGGTGACCAAAATAGAACCA
39870 TGGGAATAAT
Statistics
Matches: 116, Mismatches: 19, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
57 7 0.06
58 33 0.28
59 47 0.41
60 7 0.06
61 22 0.19
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (59 bp):
GGGTGACCAAAATAGAACCAAAATGTAACATTGAGTATGATTTTGAAAAAAAAATAATT
Found at i:42902 original size:43 final size:43
Alignment explanation
Indices: 42808--43072 Score: 300
Period size: 43 Copynumber: 6.2 Consensus size: 43
42798 TGAAAACCAA
* ** *
42808 AAACGCCGCAATAGGTCAAGATCTATAGCGGC-GTTTTGGAAC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCATTTTTGGAAC
* * * *
42850 AAACACCGCAAAAGATTAAGATCTATAGCGGCATTTTTGGAGC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCATTTTTGGAAC
* * **
42893 AAACGCCGCAAAAGGTCGAGATCTATAACGGTGTTTTTGGAAC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCATTTTTGGAAC
* * * *
42936 AAACGTCGTAAAAGGTTGAGATCTATAGCGGCGTTTTTAGAAC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCATTTTTGGAAC
* * * * * *
42979 AAACACCGTAAAAGG-TCAGATCTATAACGACATTTTTGAAAC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCATTTTTGGAAC
* *
43021 AAGCGCCGCAAAAGGTTGATATCTATAGCGGCATTTTTGGAAC
1 AAACGCCGCAAAAGGTTGAGATCTATAGCGGCATTTTTGGAAC
43064 AAACGCCGC
1 AAACGCCGC
43073 TAATTACCTT
Statistics
Matches: 184, Mismatches: 37, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
42 61 0.33
43 123 0.67
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTTGAGATCTATAGCGGCATTTTTGGAAC
Found at i:43036 original size:128 final size:128
Alignment explanation
Indices: 42826--43068 Score: 344
Period size: 128 Copynumber: 1.9 Consensus size: 128
42816 CAATAGGTCA
* * * * *
42826 AGATCTATAGCGGCGTTTTGGAACAAACACCGCAAAAGATTAAGATCTATAGCGGCATTTTTGGA
1 AGATCTATAGCGGCGTTTTAGAACAAACACCGCAAAAGAGTAAGATCTATAACGACATTTTTGAA
* **
42891 GCAAACGCCGCAAAAGGTCGAGATCTATAACGGTGTTTTTGGAACAAACGTCGTAAAAGGTTG
66 ACAAACGCCGCAAAAGGTCGAGATCTATAACGGCATTTTTGGAACAAACGTCGTAAAAGGTTG
* *
42954 AGATCTATAGCGGCGTTTTTAGAACAAACACCGTAAAAG-GTCAGATCTATAACGACATTTTTGA
1 AGATCTATAGCGGCG-TTTTAGAACAAACACCGCAAAAGAGTAAGATCTATAACGACATTTTTGA
* * * *
43018 AACAAGCGCCGCAAAAGGTTGATATCTATAGCGGCATTTTTGGAACAAACG
65 AACAAACGCCGCAAAAGGTCGAGATCTATAACGGCATTTTTGGAACAAACG
43069 CCGCTAATTA
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
128 79 0.79
129 21 0.21
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (128 bp):
AGATCTATAGCGGCGTTTTAGAACAAACACCGCAAAAGAGTAAGATCTATAACGACATTTTTGAA
ACAAACGCCGCAAAAGGTCGAGATCTATAACGGCATTTTTGGAACAAACGTCGTAAAAGGTTG
Found at i:43038 original size:85 final size:86
Alignment explanation
Indices: 42808--43072 Score: 309
Period size: 85 Copynumber: 3.1 Consensus size: 86
42798 TGAAAACCAA
* * * * * * * * *
42808 AAACGCCGCAATAGGTCAAGATCTATAGCGGC-GTTTTGGAACAAACACCGCAAAAGATTAAGAT
1 AAACACCGCAAAAGGTCGAGATCTATAACGACATTTTTGGAACAAACGCCGCAAAAGGTTGAGAT
*
42872 CTATAGCGGCATTTTTGGAGC
66 CTATAGCGGCATTTTTGGAAC
* *** * *
42893 AAACGCCGCAAAAGGTCGAGATCTATAACGGTGTTTTTGGAACAAACGTCGTAAAAGGTTGAGAT
1 AAACACCGCAAAAGGTCGAGATCTATAACGACATTTTTGGAACAAACGCCGCAAAAGGTTGAGAT
* *
42958 CTATAGCGGCGTTTTTAGAAC
66 CTATAGCGGCATTTTTGGAAC
* * * *
42979 AAACACCGTAAAAGGTC-AGATCTATAACGACATTTTTGAAACAAGCGCCGCAAAAGGTTGATAT
1 AAACACCGCAAAAGGTCGAGATCTATAACGACATTTTTGGAACAAACGCCGCAAAAGGTTGAGAT
43043 CTATAGCGGCATTTTTGGAAC
66 CTATAGCGGCATTTTTGGAAC
*
43064 AAACGCCGC
1 AAACACCGC
43073 TAATTACCTT
Statistics
Matches: 152, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
85 93 0.61
86 59 0.39
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (86 bp):
AAACACCGCAAAAGGTCGAGATCTATAACGACATTTTTGGAACAAACGCCGCAAAAGGTTGAGAT
CTATAGCGGCATTTTTGGAAC
Found at i:45674 original size:15 final size:15
Alignment explanation
Indices: 45654--45682 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45644 AAGTAAAACA
45654 TTTTTCTGAATAGTT
1 TTTTTCTGAATAGTT
45669 TTTTTCTGAATAGT
1 TTTTTCTGAATAGT
45683 GATTACAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (15 bp):
TTTTTCTGAATAGTT
Found at i:46451 original size:45 final size:45
Alignment explanation
Indices: 46387--46476 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
46377 TATACAGTGC
*
46387 ATACTATATTAAGAGTAACTAAGACT-ATATAAAAAGACAGAAAGG
1 ATACTACATTAAGAGTAACTAAGACTGA-ATAAAAAGACAGAAAGG
*
46432 ATACTACATTAAGAGTAACTAAGACTGAATAGAAAGACAGAAAGG
1 ATACTACATTAAGAGTAACTAAGACTGAATAAAAAGACAGAAAGG
46477 TAACCTCTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 41 0.98
46 1 0.02
ACGTcount: A:0.52, C:0.10, G:0.18, T:0.20
Consensus pattern (45 bp):
ATACTACATTAAGAGTAACTAAGACTGAATAAAAAGACAGAAAGG
Found at i:49731 original size:2 final size:2
Alignment explanation
Indices: 49724--49769 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
49714 GTATTTGGTT
49724 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
49767 TA T
1 TA T
49770 GCGTGAATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50366 original size:5 final size:5
Alignment explanation
Indices: 50356--50411 Score: 58
Period size: 5 Copynumber: 10.2 Consensus size: 5
50346 AATACCCGTT
*
50356 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GTTGACCC GACCC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC ---GACCC GACCC
50406 GACCC G
1 GACCC G
50412 TTGACCGTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
5 35 0.80
7 4 0.09
8 5 0.11
ACGTcount: A:0.18, C:0.52, G:0.23, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:50383 original size:17 final size:18
Alignment explanation
Indices: 50361--50417 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
50351 CCGTTGACCC
50361 GACCCGACCCGA-CCGTT
1 GACCCGACCCGACCCGTT
50378 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
50396 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
50414 GACC
1 GACC
50418 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
17 12 0.31
18 27 0.69
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:50506 original size:28 final size:28
Alignment explanation
Indices: 50435--50573 Score: 84
Period size: 29 Copynumber: 4.9 Consensus size: 28
50425 GTTGACCGAT
* ** *
50435 GCTATTCTGGGAATTAATTTGATTTTAGT
1 GCTATTTTGGGAATTAATTTGA-AATAGA
*
50464 GCTATATTGGGAATTAATTTGAAATAGA
1 GCTATTTTGGGAATTAATTTGAAATAGA
* * * *
50492 GCTATTTTGGTAATT-TTTTGAAAGAAA
1 GCTATTTTGGGAATTAATTTGAAATAGA
* * * * *
50519 G-TGATATACTAGGAATTAATTCGAAATTGGT
1 GCT-AT-T-TTGGGAATTAATTTGAAA-TAGA
*
50550 GCTATTTTGGGAATTAATTCGAAA
1 GCTATTTTGGGAATTAATTTGAAA
50574 AGGGTGTTAT
Statistics
Matches: 83, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
26 1 0.01
27 12 0.14
28 17 0.20
29 42 0.51
30 7 0.08
31 3 0.04
32 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (28 bp):
GCTATTTTGGGAATTAATTTGAAATAGA
Found at i:50562 original size:29 final size:29
Alignment explanation
Indices: 50530--50614 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
50520 TGATATACTA
**
50530 GGAATTAATTCGAAATTGGTGCTATTTTG
1 GGAATTAATTCGAAAAGGGTGCTATTTTG
*
50559 GGAATTAATTCGAAAAGGGTGTTATTTTG
1 GGAATTAATTCGAAAAGGGTGCTATTTTG
* * ** *
50588 GTAATTATTTTAAAAAGGGTACTATTT
1 GGAATTAATTCGAAAAGGGTGCTATTT
50615 GTGTAAAATG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (29 bp):
GGAATTAATTCGAAAAGGGTGCTATTTTG
Found at i:57545 original size:18 final size:18
Alignment explanation
Indices: 57522--57568 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
57512 ACCGGTCAAT
*
57522 ACCCGTTTACCCGACCCG
1 ACCCGTTGACCCGACCCG
57540 ACCCGTTGACCCGACCCG
1 ACCCGTTGACCCGACCCG
57558 ACCCGTTGACC
1 ACCCGTTGACC
57569 GTTGACCGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.49, G:0.19, T:0.15
Consensus pattern (18 bp):
ACCCGTTGACCCGACCCG
Found at i:57622 original size:29 final size:29
Alignment explanation
Indices: 57578--57737 Score: 121
Period size: 29 Copynumber: 5.6 Consensus size: 29
57568 CGTTGACCGA
* * ** *
57578 TGTTATTATGGGAATTAATTCGATTTTGG
1 TGTTATTTTGGTAATTAATTCGAAATAGG
57607 TGTTATTTTGGTAATTAATTCGAAATAGG
1 TGTTATTTTGGTAATTAATTCGAAATAGG
* **
57636 TGCTATTTTGGTAATTTTTTCGAAA-A-G
1 TGTTATTTTGGTAATTAATTCGAAATAGG
* ** * *
57663 TGATATTATAAG-AATTAATTCGAGATTGG
1 TGTTATT-TTGGTAATTAATTCGAAATAGG
* * *
57692 TGCTATTTTGGGAATTAATTC-AAAAAGGG
1 TGTTATTTTGGTAATTAATTCGAAATA-GG
*
57721 TGCTATTTTGGTAATTA
1 TGTTATTTTGGTAATTA
57738 TTTAAAAAAA
Statistics
Matches: 104, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
27 17 0.16
28 7 0.07
29 80 0.77
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (29 bp):
TGTTATTTTGGTAATTAATTCGAAATAGG
Found at i:57745 original size:29 final size:30
Alignment explanation
Indices: 57690--57758 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
57680 ATTCGAGATT
*
57690 GGTGCTATTTTGGGAATTAATT-CAAAAAG
1 GGTGCTATTTTGGGAATTAATTAAAAAAAG
* *
57719 GGTGCTATTTTGGTAATTATTTAAAAAAAG
1 GGTGCTATTTTGGGAATTAATTAAAAAAAG
*
57749 GGTACTATTT
1 GGTGCTATTT
57759 GTGTAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (30 bp):
GGTGCTATTTTGGGAATTAATTAAAAAAAG
Found at i:60090 original size:24 final size:24
Alignment explanation
Indices: 60059--60107 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
60049 ACTTTTTAAG
*
60059 GTTTTAATTCTACTTTTAGTTTTA
1 GTTTTAATACTACTTTTAGTTTTA
* *
60083 GTTTTAATACTATTTTTATTTTTA
1 GTTTTAATACTACTTTTAGTTTTA
60107 G
1 G
60108 CCGTTTCTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.63
Consensus pattern (24 bp):
GTTTTAATACTACTTTTAGTTTTA
Found at i:61405 original size:22 final size:23
Alignment explanation
Indices: 61367--61409 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
61357 CGAATTTATG
61367 AATTTTGTGATAATTTTTATTGT
1 AATTTTGTGATAATTTTTATTGT
*
61390 AATTTT-TGATATTTTTTATT
1 AATTTTGTGATAATTTTTATT
61410 TATTAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (23 bp):
AATTTTGTGATAATTTTTATTGT
Found at i:73310 original size:21 final size:21
Alignment explanation
Indices: 73269--73311 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
73259 CTTTAATTTC
*
73269 AAAATTAGAATTGAAGATTCA
1 AAAATTAGAAGTGAAGATTCA
* *
73290 AAAATTAGAAGTGGAGGTTCA
1 AAAATTAGAAGTGAAGATTCA
73311 A
1 A
73312 CAACAACAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.26
Consensus pattern (21 bp):
AAAATTAGAAGTGAAGATTCA
Found at i:73971 original size:9 final size:9
Alignment explanation
Indices: 73957--73982 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
73947 AGTTTCTATC
73957 GAGGAGATT
1 GAGGAGATT
73966 GAGGAGATT
1 GAGGAGATT
73975 GAGGAGAT
1 GAGGAGAT
73983 GTATTTCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.46, T:0.19
Consensus pattern (9 bp):
GAGGAGATT
Found at i:79572 original size:2 final size:2
Alignment explanation
Indices: 79567--79593 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
79557 TGTGAAAAAA
79567 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
79594 CATGATTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:79992 original size:21 final size:22
Alignment explanation
Indices: 79968--80011 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
79958 GAATATTCTA
* *
79968 AGAAGGAAGGAAGAGA-ATTTC
1 AGAAGAAAGAAAGAGAGATTTC
79989 AGAAGAAAGAAAGAGAGATTTC
1 AGAAGAAAGAAAGAGAGATTTC
80011 A
1 A
80012 AATGAAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.52, C:0.05, G:0.30, T:0.14
Consensus pattern (22 bp):
AGAAGAAAGAAAGAGAGATTTC
Found at i:83470 original size:323 final size:319
Alignment explanation
Indices: 82886--83527 Score: 1088
Period size: 323 Copynumber: 2.0 Consensus size: 319
82876 GTGTCACGTC
82886 ACCCATAGTGATGATGTGGTACGTGCCATATCATCAACTAAGCACATGTAAAAATGCCACATGAA
1 ACCCATAGTGATGATGTGGTACGTGCCATATCATCAACTAAGCACATGTAAAAATGCCACATGAA
* * * **
82951 CAACATGTTTTGACTGTTAGTTGACTAACGGTTTTCTTTCAACAAGAGGTATTTGTTATGAGGCT
66 CAACATGTTTTGACCGTTAGTTGACTAACGGTTCTCTTTCAACAAGAGATATTTGTTATGAACCT
*
83016 TGGTGCAGTATCTAGTCGCAAGTCTAGACGTAAAATAATTTTTGCTCTGACCTATGGTTAATCAA
131 TGGTGAAGTATCTAGTCGCAAGTCTAGACGTAAAATAATTTTTGCTCTGACCTATGGTTAATCAA
*
83081 AGAAGTAAATTCGTCCTTGACAGAACCCCTTTGTGAATAATGTTTTCTAATAGAGTGATTGCTTA
196 AGAAGTAAATTCGTCCTTGACAGAACCCCTTTGTGAATAATGTGTTCTAATAGAGTGATTGCTTA
83146 TTTTCTTTATTTAATATTAGCAGCCTTTAATAGGCCTTTAGTGACAAAAGAATAATCCT
261 TTTTCTTTATTTAATATTAGCAGCCTTTAATAGGCCTTTAGTGACAAAAGAATAATCCT
*
83205 ACCCATAGTGATGATGTGGTACGTGCCATATCATCAATTAAGCACATGTAAAAATGCCACATGAA
1 ACCCATAGTGATGATGTGGTACGTGCCATATCATCAACTAAGCACATGTAAAAATGCCACATGAA
*** * *
83270 CATGTTTTTTTTTTTGACCGTTAGTTGACTAACGGTTCTCTTTCAACAGGAGATATTTGTTATGA
66 CA----ACATGTTTTGACCGTTAGTTGACTAACGGTTCTCTTTCAACAAGAGATATTTGTTATGA
*
83335 ACCTTGGTATAAG-ATCTAGTCGCAAGTCTAGACGTAAAATAATTTTTGCTCTGACCTATGGTTA
127 ACCTTGGT-GAAGTATCTAGTCGCAAGTCTAGACGTAAAATAATTTTTGCTCTGACCTATGGTTA
*
83399 ATCAAAGAAGTAAATTCGTCCTTGACAGAACCCTTTTGTGAATAATGTGTTCTAATAGAGTGATT
191 ATCAAAGAAGTAAATTCGTCCTTGACAGAACCCCTTTGTGAATAATGTGTTCTAATAGAGTGATT
*
83464 GCTTATTTTCTTTATTTAATATTAGCAGCCTTTAGTAGGCCTTTAGTGACAAAAGAATAATCCT
256 GCTTATTTTCTTTATTTAATATTAGCAGCCTTTAATAGGCCTTTAGTGACAAAAGAATAATCCT
83528 GATGAAAATA
Statistics
Matches: 302, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
319 66 0.22
323 234 0.77
324 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (319 bp):
ACCCATAGTGATGATGTGGTACGTGCCATATCATCAACTAAGCACATGTAAAAATGCCACATGAA
CAACATGTTTTGACCGTTAGTTGACTAACGGTTCTCTTTCAACAAGAGATATTTGTTATGAACCT
TGGTGAAGTATCTAGTCGCAAGTCTAGACGTAAAATAATTTTTGCTCTGACCTATGGTTAATCAA
AGAAGTAAATTCGTCCTTGACAGAACCCCTTTGTGAATAATGTGTTCTAATAGAGTGATTGCTTA
TTTTCTTTATTTAATATTAGCAGCCTTTAATAGGCCTTTAGTGACAAAAGAATAATCCT
Found at i:104375 original size:18 final size:18
Alignment explanation
Indices: 104352--104386 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
104342 AAATTTTTAG
*
104352 ATCTTCCACCTCATCATT
1 ATCTTCCACATCATCATT
*
104370 ATCTTCCTCATCATCAT
1 ATCTTCCACATCATCAT
104387 AATTTGGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.37, G:0.00, T:0.40
Consensus pattern (18 bp):
ATCTTCCACATCATCATT
Found at i:116162 original size:16 final size:16
Alignment explanation
Indices: 116138--116168 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
116128 TCTAATTTTT
*
116138 TTTTTGAGTTCAAGTC
1 TTTTCGAGTTCAAGTC
116154 TTTTCGAGTTCAAGT
1 TTTTCGAGTTCAAGT
116169 TTCAATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTCGAGTTCAAGTC
Done.